[Chimera-users] Three suggestions

Eric Pettersen pett at cgl.ucsf.edu
Wed Apr 10 16:24:27 PDT 2013

Hi Antoine,

On Apr 10, 2013, at 9:54 AM, Antoine Maillard wrote:

> Dear Eric,
> Thank you for your replies and your quick implementation of an automated refresh for named selections!
> Concerning suggestion #1:   changing Chain ID of a portion of a chain was meant to assist matchmaker in targeting the right domain and not let it take adventice (meaningless) pieces into account. I realize now that this could be quiet a challenge for Chimera to interpret in all the procedures already available... and will stick to the cut-into-domains-of-interest approach.

Yeah, as Elaine mentioned, the "restrict to selection" feature was implemented for exactly this reason -- matching domains embedded in longer chains.

> About suggestion #2: the ~namesel command that you proposed would allow to edit the listing, which is sometimes useful, i.e.  when you happen to get more and more named selections, sometimes similar in different models, and realize the names given were not specific enough. That would be nice!

Okay, I've implement a ~namesel command.  It will be in the next daily build.

> Suggestion #3: if this is a problem then leave it where it stands!
> (In case it is not: would it sound more reasonable to offer the window-size memorization as a tickable option? Could the window-location memorization and the tiling be combined when the "same" window is to be opened more than once?)

Memorizing the window size is more feasible / has less pitfalls than memorizing the position.  Even then only certain dialogs can actually be distinguished by Chimera.  In Python, such dialogs have "name" attributes so that any tool can ask for that dialog to be shown (e.g. Model Panel, Volume Viewer) whereas other dialogs are essentially nameless (e.g. Sequence dialogs, CASTp dialogs).  Sizes for named dialogs could conceivably be remembered.  Even then there are a lot of limitations / pitfalls.  Two that occur to me immediately are:  you probably only want to restore a memorized size if it's larger than the dialog's "natural" size -- otherwise various interface elements will be clipped away, and if those elements are brand new because the tool was improved then the user might never become aware of them(!);  the other is that you probably don't want to memorize size changes for some dialogs -- because they became larger to show more data (I'm thinking Volume Viewer here) and will be uselessly larger when shown in another context with less data.

I don't know.  If some more people ask for the same thing I might bite the bullet.  Otherwise, I'll stick to my plan of implementing size remembrance on a dialog-by-dialog basis.  Initially just the Model Panel.


                        Eric Pettersen
                        UCSF Computer Graphics Lab

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